it is rare that a cutting board comes out of the clamps perfectly flat on both faces. i have a scrap piece of granite countertop material (the cut out for the cook top in our kitchen) that i use to test flatness. if it rocks, i mark the high spots with chalk and then sand them down with the belt sander. test again, and repeat as needed until the face sits flat, then do the other face, same process. that way, the cutting board won't rock on your counter top when you use it. this can take anywhere from 10 minutes to a frustrating hour, and consume several sanding belts and sanding disks.
i have seen videos of others running their end grain cutting boards thru a planer or flat bed sander, but if you don't take precautions, you'll get tearout on the trailing edge, and ruin the last 1-2" of the board. and that assumes the face that is down is flat too, which is a poor assumption. my method works for me.
